The only thing I can think of would be a IRQ conflict, as in your using a component in a shared IRQ resource that is causing an issue with the PIC-e X16 slot.
I guess it's possible for the cpu to have an issue with a pci-e slot, but if it had a problem with one slot I would expect it to have a problem with all of them. You have two LGA1155 systems? Try the cpu, from the problem system, in the good system.